The Unequal Area Facility Layout Problem (UA-FLP) is a relevant optimization problem related to industrial design, that deals with obtaining the most effective allocation of facilities, that make up the rectangular manufacturing plant layout. The UA-FLP is known to be a hard optimization problem, where meta-heuristic approaches are a good option to obtain competitive solutions. Many of these computational approaches, however, usually fall into local optima, and suffer from lack of diversity in their population, mainly due to the huge search spaces and hard fitness landscapes produced by the traditional representation of UA-FLP. To solve these issues, in this paper we propose a novel hybrid meta-heuristic approach, which combines a Coral Reefs Optimization algorithm (CRO) with a Variable Neighborhood Search (VNS) and a new representation for the problem, called Relaxed Flexible Bay Structure (RFBS), which simplifies the encoding and makes its fitness landscape more affordable. Thus, the use of VNS allows more intensive exploitation of the searching space with an affordable computational cost, as well as the RFBS allows better management of the free space into the plant layout. This combined strategy has been tested over a set of UA-FLP instances of different sizes, which have been previously tackled in the literature with alternative meta-heuristics. The tests results show very good performance in all cases.